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This page was generated on 2025-08-27 12:03 -0400 (Wed, 27 Aug 2025).

HostnameOSArch (*)R versionInstalled pkgs
nebbiolo2Linux (Ubuntu 24.04.3 LTS)x86_644.5.1 (2025-06-13) -- "Great Square Root" 4822
lconwaymacOS 12.7.1 Montereyx86_644.5.1 (2025-06-13) -- "Great Square Root" 4612
kjohnson3macOS 13.7.7 Venturaarm644.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" 4555
taishanLinux (openEuler 24.03 LTS)aarch644.5.0 (2025-04-11) -- "How About a Twenty-Six" 4539
Click on any hostname to see more info about the system (e.g. compilers)      (*) as reported by 'uname -p', except on Windows and Mac OS X

Package 797/2319HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
gemma.R 3.5.4  (landing page)
Ogan Mancarci
Snapshot Date: 2025-08-26 13:45 -0400 (Tue, 26 Aug 2025)
git_url: https://git.bioconductor.org/packages/gemma.R
git_branch: devel
git_last_commit: 73d1354
git_last_commit_date: 2025-06-23 21:53:56 -0400 (Mon, 23 Jun 2025)
nebbiolo2Linux (Ubuntu 24.04.3 LTS) / x86_64  OK    ERROR  skipped
lconwaymacOS 12.7.1 Monterey / x86_64  OK    ERROR  skippedskipped
kjohnson3macOS 13.7.7 Ventura / arm64  OK    ERROR  skippedskipped
taishanLinux (openEuler 24.03 LTS) / aarch64  OK    ERROR  skipped


BUILD results for gemma.R on nebbiolo2

To the developers/maintainers of the gemma.R package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/gemma.R.git to reflect on this report. See Troubleshooting Build Report for more information.
- Use the following Renviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information.

raw results


Summary

Package: gemma.R
Version: 3.5.4
Command: /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 gemma.R
StartedAt: 2025-08-26 17:24:14 -0400 (Tue, 26 Aug 2025)
EndedAt: 2025-08-26 17:26:51 -0400 (Tue, 26 Aug 2025)
EllapsedTime: 157.2 seconds
RetCode: 1
Status:   ERROR  
PackageFile: None
PackageFileSize: NA

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.22-bioc/R/bin/R CMD build --keep-empty-dirs --no-resave-data --md5 gemma.R
###
##############################################################################
##############################################################################


* checking for file ‘gemma.R/DESCRIPTION’ ... OK
* preparing ‘gemma.R’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... ERROR
--- re-building ‘gemma.R.Rmd’ using rmarkdown

Quitting from gemma.R.Rmd:325-328 [unnamed-chunk-15]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `.body()`:
! https://gemma.msl.ubc.ca/rest/v2/resultSets/550248
500: Internal server error.
---
Backtrace:
     ▆
  1. └─gemma.R::get_differential_expression_values("GSE46416")
  2.   └─base::lapply(...)
  3.     └─gemma.R (local) FUN(X[[i]], ...)
  4.       └─gemma.R:::.getResultSets(x, memoised = memoised)
  5.         └─gemma.R:::mem.getResultSets(...)
  6.           ├─gemma.R (local) mem_call(...)
  7.           │ ├─base::withVisible(eval(mc, parent.frame()))
  8.           │ └─base::eval(mc, parent.frame())
  9.           │   └─base::eval(mc, parent.frame())
 10.           └─gemma.R (local) `<fn>`(...)
 11.             └─gemma.R:::.body(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'gemma.R.Rmd' failed with diagnostics:
https://gemma.msl.ubc.ca/rest/v2/resultSets/550248
500: Internal server error.
--- failed re-building ‘gemma.R.Rmd’

--- re-building ‘metadata.Rmd’ using rmarkdown

Quitting from metadata.Rmd:131-142 [unnamed-chunk-6]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `sum()`:
! invalid 'type' (list) of argument
---
Backtrace:
    ▆
 1. └─... %>% sum
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'metadata.Rmd' failed with diagnostics:
invalid 'type' (list) of argument
--- failed re-building ‘metadata.Rmd’

--- re-building ‘metanalysis.Rmd’ using rmarkdown

Quitting from metanalysis.Rmd:225-238 [unnamed-chunk-13]
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
<error/rlang_error>
Error in `.body()`:
! https://gemma.msl.ubc.ca/rest/v2/resultSets/515364
500: Internal server error.
---
Backtrace:
     ▆
  1. ├─parkin_contrasts$result.ID %>% ...
  2. ├─BiocGenerics::lapply(...)
  3. └─base::lapply(...)
  4.   └─FUN(X[[i]], ...)
  5.     └─gemma.R::get_differential_expression_values(resultSets = x)
  6.       └─base::lapply(...)
  7.         └─gemma.R (local) FUN(X[[i]], ...)
  8.           └─gemma.R:::.getResultSets(x, memoised = memoised)
  9.             └─gemma.R:::mem.getResultSets(...)
 10.               ├─gemma.R (local) mem_call(...)
 11.               │ ├─base::withVisible(eval(mc, parent.frame()))
 12.               │ └─base::eval(mc, parent.frame())
 13.               │   └─base::eval(mc, parent.frame())
 14.               └─gemma.R (local) `<fn>`(...)
 15.                 └─gemma.R:::.body(...)
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

Error: processing vignette 'metanalysis.Rmd' failed with diagnostics:
https://gemma.msl.ubc.ca/rest/v2/resultSets/515364
500: Internal server error.
--- failed re-building ‘metanalysis.Rmd’

SUMMARY: processing the following files failed:
  ‘gemma.R.Rmd’ ‘metadata.Rmd’ ‘metanalysis.Rmd’

Error: Vignette re-building failed.
Execution halted